NOVOALIGN

[GoogleCodeExporter]

Hi Sam,

a conceptual  question as I have never used Novoalign before. WHat is the Index 
file name? Because The moidule is validated ok, but I have these errors:

-NOVO INDEX

===Pipeline Errors===
Error encountered while trying to execute 
/projects1/Alignment/Novoalign/novoindex.sh 
/projects1/test_pipeline/NEW_ORGANIZATION/Aligners/NOVOALIGN/SE indexfile 
/projects1/Reference_genomes/hg18_ensembl/gatk-canonical/gatk-hg18_ensembl.fa 
instance 1      

-NOVO ALIGN

# novoalign (V2.07.13 - Build Jul 18 2011 @ 09:03:08 - A short read aligner 
with qualities.
# (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd.
# novoalign.lic file not found.
# Licensed for evaluation, educational, and not-for-profit use only.
#  novoalign -d indexfile -f 
/projects2/USC/canonical-test-data/hg18_ensembl-bwa/mini-bam/s_1_1_sequence.150k
.txt 
/projects2/USC/canonical-test-data/hg18_ensembl-bwa/mini-bam/s_1_2_sequence.150k
.txt -F ILMFQ -o SAM 
# Starting at Fri Sep  9 14:52:03 2011
# Interpreting input files as Illumina FASTQ, Casava Pipeline 1.3 to 1.7.
Bad file descriptor
Error opening file indexfile


I attach the pipe I have mosified to use if from my local client.

Fed      

Original issue reported on code.google.com by [email protected] on 9 Sep 2011 at 10:01

Attachments:

• Novoalign_UCI.pipe